Starting phenix.real_space_refine on Fri Jun 20 12:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uty_42553/06_2025/8uty_42553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uty_42553/06_2025/8uty_42553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uty_42553/06_2025/8uty_42553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uty_42553/06_2025/8uty_42553.map" model { file = "/net/cci-nas-00/data/ceres_data/8uty_42553/06_2025/8uty_42553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uty_42553/06_2025/8uty_42553.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 4 5.21 5 S 152 5.16 5 C 14846 2.51 5 N 4067 2.21 5 O 4677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23765 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "I" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Conformer: "B" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} bond proxies already assigned to first conformer: 3444 Chain: "K" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3039 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain: "S" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3503 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 20, 'TRANS': 428} Chain: "N" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3048 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.49 residue: pdb=" N AALA B 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.49 residue: pdb=" N AASP B 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.49 residue: pdb=" N AGLU B 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.49 residue: pdb=" N ATHR I 429 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.49 residue: pdb=" N AALA I 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.49 residue: pdb=" N AASP I 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.49 residue: pdb=" N AGLU I 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.49 residue: pdb=" N AGLN I 433 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.49 Time building chain proxies: 17.18, per 1000 atoms: 0.72 Number of scatterers: 23765 At special positions: 0 Unit cell: (104, 115.7, 240.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 152 16.00 P 19 15.00 Mg 4 11.99 O 4677 8.00 N 4067 7.00 C 14846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 4.1 seconds 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 23 sheets defined 49.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.384A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.349A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 4.639A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 113 through 129 removed outlier: 4.148A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.101A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.539A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.569A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.953A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.931A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.747A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.118A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.330A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.701A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.147A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.858A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.596A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.001A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 removed outlier: 3.609A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.835A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.657A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 424 removed outlier: 3.653A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.724A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.577A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.569A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.587A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.585A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.017A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.822A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.823A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.033A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.142A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 3.825A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.660A pdb=" N GLN I 43 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.120A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.539A pdb=" N ILE I 84 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 126 removed outlier: 3.842A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 180 through 195 removed outlier: 3.958A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.537A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 4.099A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 282 removed outlier: 4.167A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG I 282 " --> pdb=" O GLN I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 295 Processing helix chain 'I' and resid 296 through 299 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.644A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.529A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 424 removed outlier: 3.922A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 88 removed outlier: 4.251A pdb=" N GLU K 79 " --> pdb=" O ARG K 75 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 removed outlier: 3.558A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 296 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 353 removed outlier: 4.007A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 removed outlier: 4.667A pdb=" N ILE K 369 " --> pdb=" O ASN K 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 3.676A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 80 removed outlier: 3.922A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 129 Processing helix chain 'S' and resid 144 through 161 removed outlier: 5.612A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 190 Processing helix chain 'S' and resid 190 through 197 Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.541A pdb=" N LEU S 227 " --> pdb=" O THR S 223 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 243 No H-bonds generated for 'chain 'S' and resid 241 through 243' Processing helix chain 'S' and resid 251 through 260 removed outlier: 3.575A pdb=" N VAL S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.037A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 296 removed outlier: 3.654A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 301 removed outlier: 3.626A pdb=" N GLN S 301 " --> pdb=" O PRO S 298 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 338 removed outlier: 3.588A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 4.004A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 412 removed outlier: 3.720A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 415 through 437 removed outlier: 4.176A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL S 437 " --> pdb=" O GLU S 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 87 Processing helix chain 'N' and resid 102 through 109 Processing helix chain 'N' and resid 117 through 134 Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.688A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 295 removed outlier: 3.785A pdb=" N ASP N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) Proline residue: N 292 - end of helix Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 349 Processing helix chain 'N' and resid 363 through 386 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.709A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.155A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.933A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.618A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AA9, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.094A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU I 3 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY I 132 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER I 138 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE I 163 " --> pdb=" O CYS I 129 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 14.020A pdb=" N ASP I 203 " --> pdb=" O PHE I 270 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 57 removed outlier: 3.535A pdb=" N TYR K 54 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 54 through 57 removed outlier: 3.535A pdb=" N TYR K 54 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AB7, first strand: chain 'S' and resid 65 through 68 removed outlier: 7.805A pdb=" N GLU S 3 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE S 135 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE S 5 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL S 137 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE S 7 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N HIS S 139 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL S 9 " --> pdb=" O HIS S 139 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N HIS S 139 " --> pdb=" O ILE S 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'S' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.320A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.320A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AC5, first strand: chain 'N' and resid 205 through 206 1185 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.54 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4419 1.33 - 1.45: 6156 1.45 - 1.57: 13402 1.57 - 1.70: 43 1.70 - 1.82: 242 Bond restraints: 24262 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" N LYS K 297 " pdb=" CA LYS K 297 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.29e-02 6.01e+03 3.03e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 24257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 32491 3.37 - 6.74: 412 6.74 - 10.11: 21 10.11 - 13.48: 5 13.48 - 16.85: 3 Bond angle restraints: 32932 Sorted by residual: angle pdb=" O ALA I 428 " pdb=" C ALA I 428 " pdb=" N BTHR I 429 " ideal model delta sigma weight residual 122.59 106.09 16.50 1.33e+00 5.65e-01 1.54e+02 angle pdb=" N ILE S 114 " pdb=" CA ILE S 114 " pdb=" C ILE S 114 " ideal model delta sigma weight residual 112.96 107.20 5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" PB ANP N 501 " pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 126.95 110.10 16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 110.94 16.01 3.00e+00 1.11e-01 2.85e+01 angle pdb=" N AASP B 431 " pdb=" CA AASP B 431 " pdb=" C AASP B 431 " ideal model delta sigma weight residual 110.80 121.69 -10.89 2.13e+00 2.20e-01 2.61e+01 ... (remaining 32927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 14206 35.34 - 70.69: 444 70.69 - 106.03: 68 106.03 - 141.38: 19 141.38 - 176.72: 7 Dihedral angle restraints: 14744 sinusoidal: 6096 harmonic: 8648 Sorted by residual: dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 84.15 176.72 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -115.37 -175.36 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' GTP S 501 " pdb=" O5' GTP S 501 " pdb=" PA GTP S 501 " pdb=" O3A GTP S 501 " ideal model delta sinusoidal sigma weight residual 69.27 -81.01 150.28 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 14741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2807 0.053 - 0.105: 595 0.105 - 0.158: 178 0.158 - 0.210: 29 0.210 - 0.263: 7 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C3' ANP N 501 " pdb=" C2' ANP N 501 " pdb=" C4' ANP N 501 " pdb=" O3' ANP N 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA GLN I 375 " pdb=" N GLN I 375 " pdb=" C GLN I 375 " pdb=" CB GLN I 375 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3613 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 428 " 0.086 2.00e-02 2.50e+03 1.60e-01 2.55e+02 pdb=" C ALA I 428 " -0.276 2.00e-02 2.50e+03 pdb=" O ALA I 428 " 0.099 2.00e-02 2.50e+03 pdb=" N BTHR I 429 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 428 " 0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C ALA I 428 " -0.091 2.00e-02 2.50e+03 pdb=" O ALA I 428 " 0.034 2.00e-02 2.50e+03 pdb=" N ATHR I 429 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 295 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C ASN N 295 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN N 295 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS N 296 " 0.021 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 147 2.53 - 3.12: 18418 3.12 - 3.72: 36689 3.72 - 4.31: 50731 4.31 - 4.90: 86385 Nonbonded interactions: 192370 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.941 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.954 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.964 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.968 2.170 nonbonded pdb=" OG SER K 104 " pdb="MG MG K 501 " model vdw 1.972 2.170 ... (remaining 192365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) selection = (chain 'S' and (resid 1 through 440 or resid 501 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 428 or resid 501 or resid 502)) selection = (chain 'I' and (resid 1 through 428 or resid 501 or resid 502)) } ncs_group { reference = (chain 'K' and resid 4 through 389) selection = (chain 'N' and resid 4 through 389) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 58.430 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 24262 Z= 0.312 Angle : 0.883 16.847 32932 Z= 0.496 Chirality : 0.050 0.263 3616 Planarity : 0.006 0.160 4281 Dihedral : 18.432 176.724 9196 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.81 % Allowed : 4.38 % Favored : 94.81 % Rotamer: Outliers : 1.45 % Allowed : 14.19 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 2974 helix: 1.09 (0.15), residues: 1238 sheet: -0.29 (0.22), residues: 508 loop : -1.14 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 388 HIS 0.004 0.001 HIS N 59 PHE 0.017 0.001 PHE K 86 TYR 0.045 0.001 TYR E 24 ARG 0.015 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.14290 ( 1118) hydrogen bonds : angle 5.95510 ( 3417) covalent geometry : bond 0.00554 (24262) covalent geometry : angle 0.88254 (32932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 502 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8944 (m-40) cc_final: 0.8731 (m-40) REVERT: A 254 GLU cc_start: 0.4307 (mm-30) cc_final: 0.3620 (mm-30) REVERT: B 203 ASP cc_start: 0.8114 (t0) cc_final: 0.7714 (t0) REVERT: E 51 THR cc_start: 0.8856 (p) cc_final: 0.8636 (t) REVERT: E 120 ASP cc_start: 0.8302 (t0) cc_final: 0.8095 (m-30) REVERT: E 322 ASP cc_start: 0.8721 (t0) cc_final: 0.8181 (t0) REVERT: I 67 ASP cc_start: 0.8165 (t70) cc_final: 0.7940 (t70) REVERT: I 291 GLN cc_start: 0.8356 (tp40) cc_final: 0.8003 (tp40) REVERT: I 359 ARG cc_start: 0.8844 (tpt-90) cc_final: 0.8586 (mmm-85) REVERT: I 374 ILE cc_start: 0.9172 (tp) cc_final: 0.8876 (tt) REVERT: I 424 GLN cc_start: 0.8677 (tt0) cc_final: 0.8354 (tt0) REVERT: K 26 CYS cc_start: 0.8843 (p) cc_final: 0.8477 (m) REVERT: K 67 TYR cc_start: 0.7897 (t80) cc_final: 0.7224 (t80) REVERT: K 74 TYR cc_start: 0.8462 (t80) cc_final: 0.7955 (t80) REVERT: K 83 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8492 (tp-100) REVERT: K 87 GLU cc_start: 0.8698 (mp0) cc_final: 0.8097 (mp0) REVERT: K 105 TYR cc_start: 0.8516 (t80) cc_final: 0.8113 (t80) REVERT: K 189 TYR cc_start: 0.7750 (t80) cc_final: 0.7268 (t80) REVERT: K 285 LEU cc_start: 0.7735 (mp) cc_final: 0.7398 (mm) REVERT: K 290 SER cc_start: 0.7322 (OUTLIER) cc_final: 0.7004 (p) REVERT: K 301 THR cc_start: 0.6461 (OUTLIER) cc_final: 0.6139 (p) REVERT: K 367 LYS cc_start: 0.9572 (ttpp) cc_final: 0.9313 (pttm) REVERT: S 166 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8518 (mtpp) REVERT: S 228 ASN cc_start: 0.9030 (m-40) cc_final: 0.8731 (m-40) REVERT: S 326 LYS cc_start: 0.8882 (pptt) cc_final: 0.8635 (pttm) REVERT: N 20 MET cc_start: 0.8427 (mtm) cc_final: 0.7930 (mtm) REVERT: N 148 GLU cc_start: 0.8226 (pt0) cc_final: 0.8019 (tt0) REVERT: N 180 ASP cc_start: 0.7576 (t0) cc_final: 0.7095 (t0) REVERT: N 217 SER cc_start: 0.9201 (p) cc_final: 0.8740 (p) REVERT: N 248 ASP cc_start: 0.8031 (t0) cc_final: 0.7685 (t0) outliers start: 30 outliers final: 5 residues processed: 529 average time/residue: 0.3832 time to fit residues: 309.1289 Evaluate side-chains 469 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 462 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 299 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain S residue 447 GLU Chi-restraints excluded: chain N residue 44 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 140 optimal weight: 0.0670 chunk 172 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN E 31 GLN E 107 HIS E 128 GLN E 358 GLN I 131 GLN I 423 GLN S 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.119248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091625 restraints weight = 48726.219| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.90 r_work: 0.3205 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24262 Z= 0.121 Angle : 0.597 10.455 32932 Z= 0.297 Chirality : 0.044 0.349 3616 Planarity : 0.004 0.048 4281 Dihedral : 12.822 178.517 3616 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.10 % Favored : 96.63 % Rotamer: Outliers : 2.07 % Allowed : 13.95 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 2974 helix: 1.71 (0.15), residues: 1250 sheet: -0.11 (0.22), residues: 546 loop : -0.96 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 21 HIS 0.004 0.001 HIS K 84 PHE 0.012 0.001 PHE K 94 TYR 0.033 0.001 TYR E 24 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 1118) hydrogen bonds : angle 4.31193 ( 3417) covalent geometry : bond 0.00260 (24262) covalent geometry : angle 0.59675 (32932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 485 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8010 (t0) cc_final: 0.7774 (t0) REVERT: B 203 ASP cc_start: 0.8083 (t0) cc_final: 0.7760 (t0) REVERT: B 288 GLU cc_start: 0.8258 (mp0) cc_final: 0.7865 (mp0) REVERT: B 291 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7895 (tp-100) REVERT: E 117 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7694 (tt) REVERT: E 123 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8243 (ttm-80) REVERT: I 131 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: I 155 ILE cc_start: 0.9034 (mt) cc_final: 0.8700 (mm) REVERT: I 267 MET cc_start: 0.8813 (mtp) cc_final: 0.8520 (mtp) REVERT: I 374 ILE cc_start: 0.9349 (tp) cc_final: 0.8987 (tt) REVERT: I 424 GLN cc_start: 0.8828 (tt0) cc_final: 0.8624 (tt0) REVERT: K 26 CYS cc_start: 0.8960 (p) cc_final: 0.8503 (m) REVERT: K 74 TYR cc_start: 0.8516 (t80) cc_final: 0.8058 (t80) REVERT: K 83 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8485 (tp-100) REVERT: K 193 GLN cc_start: 0.8221 (tp40) cc_final: 0.7978 (tm-30) REVERT: K 327 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7794 (tpp) REVERT: S 1 MET cc_start: 0.6485 (pmm) cc_final: 0.6125 (pmm) REVERT: S 27 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8239 (mt-10) REVERT: S 69 ASP cc_start: 0.7859 (t0) cc_final: 0.7442 (t0) REVERT: S 120 ASP cc_start: 0.8413 (t0) cc_final: 0.8159 (t0) REVERT: S 121 ARG cc_start: 0.6594 (ttt-90) cc_final: 0.5902 (tpt-90) REVERT: S 154 MET cc_start: 0.9130 (mmm) cc_final: 0.8867 (mmm) REVERT: S 220 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8408 (tp30) REVERT: S 259 LEU cc_start: 0.8808 (mp) cc_final: 0.8602 (mp) REVERT: S 326 LYS cc_start: 0.8829 (pptt) cc_final: 0.8537 (pttp) REVERT: S 411 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7585 (mm-30) REVERT: S 447 GLU cc_start: 0.2393 (OUTLIER) cc_final: 0.1958 (pp20) REVERT: N 20 MET cc_start: 0.8606 (mtm) cc_final: 0.8099 (mtm) REVERT: N 217 SER cc_start: 0.8933 (p) cc_final: 0.8657 (p) REVERT: N 248 ASP cc_start: 0.8303 (t0) cc_final: 0.7693 (t0) REVERT: N 295 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6954 (p0) REVERT: N 346 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8580 (mtp85) outliers start: 46 outliers final: 23 residues processed: 509 average time/residue: 0.5372 time to fit residues: 425.3769 Evaluate side-chains 477 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 449 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 447 GLU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 266 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 245 GLN E 128 GLN I 100 ASN I 131 GLN I 384 GLN K 116 GLN ** K 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 HIS N 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.115954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.089027 restraints weight = 37864.576| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.49 r_work: 0.3247 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24262 Z= 0.117 Angle : 0.558 8.806 32932 Z= 0.278 Chirality : 0.044 0.463 3616 Planarity : 0.004 0.048 4281 Dihedral : 10.123 177.187 3608 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.20 % Favored : 96.59 % Rotamer: Outliers : 2.62 % Allowed : 14.81 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2974 helix: 1.91 (0.15), residues: 1249 sheet: 0.04 (0.22), residues: 538 loop : -0.91 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.003 0.001 HIS N 59 PHE 0.014 0.001 PHE N 15 TYR 0.025 0.001 TYR E 24 ARG 0.010 0.000 ARG K 254 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1118) hydrogen bonds : angle 4.07920 ( 3417) covalent geometry : bond 0.00255 (24262) covalent geometry : angle 0.55754 (32932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 466 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 GLU cc_start: 0.7340 (mp0) cc_final: 0.7000 (mt-10) REVERT: A 396 ASP cc_start: 0.8467 (m-30) cc_final: 0.8229 (m-30) REVERT: B 26 ASP cc_start: 0.8772 (t0) cc_final: 0.8533 (t0) REVERT: B 203 ASP cc_start: 0.8200 (t0) cc_final: 0.7883 (t0) REVERT: B 288 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: B 291 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8042 (tp-100) REVERT: E 24 TYR cc_start: 0.8371 (m-80) cc_final: 0.7464 (m-80) REVERT: E 123 ARG cc_start: 0.8898 (ttp-110) cc_final: 0.8406 (ttm-80) REVERT: E 413 MET cc_start: 0.7920 (mtm) cc_final: 0.7646 (mtp) REVERT: I 31 ASP cc_start: 0.8374 (t70) cc_final: 0.8052 (t0) REVERT: I 131 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: I 155 ILE cc_start: 0.9109 (mt) cc_final: 0.8812 (mm) REVERT: I 226 ASN cc_start: 0.8839 (m-40) cc_final: 0.8386 (m110) REVERT: I 267 MET cc_start: 0.8965 (mtp) cc_final: 0.8700 (mtp) REVERT: I 374 ILE cc_start: 0.9401 (tp) cc_final: 0.9060 (tt) REVERT: K 19 GLU cc_start: 0.8469 (mp0) cc_final: 0.7759 (mt-10) REVERT: K 26 CYS cc_start: 0.8965 (p) cc_final: 0.8515 (m) REVERT: K 74 TYR cc_start: 0.8519 (t80) cc_final: 0.8085 (t80) REVERT: K 83 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8340 (tp-100) REVERT: K 183 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8741 (ttpp) REVERT: K 193 GLN cc_start: 0.8351 (tp40) cc_final: 0.7644 (tm-30) REVERT: K 197 ASP cc_start: 0.8410 (t0) cc_final: 0.8090 (m-30) REVERT: K 317 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7695 (tp30) REVERT: K 324 ARG cc_start: 0.8780 (mtp-110) cc_final: 0.8236 (mtt180) REVERT: K 327 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7949 (tpp) REVERT: S 1 MET cc_start: 0.6580 (pmm) cc_final: 0.6366 (pmm) REVERT: S 27 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8364 (mt-10) REVERT: S 120 ASP cc_start: 0.8603 (t0) cc_final: 0.8287 (t0) REVERT: S 121 ARG cc_start: 0.6704 (ttt-90) cc_final: 0.6086 (tpt-90) REVERT: S 154 MET cc_start: 0.9175 (mmm) cc_final: 0.8957 (mmm) REVERT: S 220 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8523 (tp30) REVERT: S 228 ASN cc_start: 0.9146 (m-40) cc_final: 0.8857 (m-40) REVERT: S 259 LEU cc_start: 0.8905 (mp) cc_final: 0.8693 (mp) REVERT: S 279 GLU cc_start: 0.8741 (tp30) cc_final: 0.8485 (tp30) REVERT: S 326 LYS cc_start: 0.8895 (pptt) cc_final: 0.8621 (pttp) REVERT: S 411 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7853 (mm-30) REVERT: S 417 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8221 (mt-10) REVERT: N 20 MET cc_start: 0.8657 (mtm) cc_final: 0.8163 (mtm) REVERT: N 148 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: N 210 MET cc_start: 0.4747 (ppp) cc_final: 0.4382 (ppp) REVERT: N 217 SER cc_start: 0.8974 (p) cc_final: 0.8437 (p) REVERT: N 248 ASP cc_start: 0.8454 (t0) cc_final: 0.7775 (t0) REVERT: N 282 ILE cc_start: 0.8863 (pt) cc_final: 0.8384 (mt) REVERT: N 295 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7326 (p0) REVERT: N 346 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8275 (mtp85) outliers start: 59 outliers final: 34 residues processed: 502 average time/residue: 0.3503 time to fit residues: 273.4360 Evaluate side-chains 488 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 449 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 283 SER Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 52 PHE Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 244 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 100 ASN I 131 GLN K 83 GLN K 366 ASN S 197 HIS N 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.117791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090885 restraints weight = 41394.179| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.63 r_work: 0.3209 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24262 Z= 0.131 Angle : 0.553 9.137 32932 Z= 0.275 Chirality : 0.044 0.324 3616 Planarity : 0.004 0.047 4281 Dihedral : 9.383 178.019 3605 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Rotamer: Outliers : 2.50 % Allowed : 15.55 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 2974 helix: 2.01 (0.15), residues: 1249 sheet: 0.15 (0.22), residues: 533 loop : -0.89 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.003 0.001 HIS A 283 PHE 0.018 0.001 PHE B 367 TYR 0.021 0.001 TYR E 24 ARG 0.006 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1118) hydrogen bonds : angle 4.00240 ( 3417) covalent geometry : bond 0.00294 (24262) covalent geometry : angle 0.55319 (32932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 472 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7858 (pm20) cc_final: 0.7227 (pm20) REVERT: A 69 ASP cc_start: 0.8125 (t0) cc_final: 0.7770 (t0) REVERT: A 154 MET cc_start: 0.8842 (mmm) cc_final: 0.8486 (mmm) REVERT: A 215 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7937 (ttp-110) REVERT: A 254 GLU cc_start: 0.3813 (mm-30) cc_final: 0.2157 (mm-30) REVERT: A 284 GLU cc_start: 0.7085 (mp0) cc_final: 0.6770 (mt-10) REVERT: A 396 ASP cc_start: 0.8342 (m-30) cc_final: 0.8024 (m-30) REVERT: B 203 ASP cc_start: 0.8019 (t0) cc_final: 0.7711 (t0) REVERT: B 288 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: B 291 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7870 (tp-100) REVERT: E 24 TYR cc_start: 0.8217 (m-80) cc_final: 0.7420 (m-80) REVERT: E 123 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8218 (ttm-80) REVERT: I 31 ASP cc_start: 0.8193 (t70) cc_final: 0.7841 (t0) REVERT: I 131 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: I 155 ILE cc_start: 0.9024 (mt) cc_final: 0.8721 (mm) REVERT: I 230 SER cc_start: 0.8911 (m) cc_final: 0.8587 (t) REVERT: I 374 ILE cc_start: 0.9337 (tp) cc_final: 0.9037 (tt) REVERT: I 424 GLN cc_start: 0.8866 (tt0) cc_final: 0.8578 (tt0) REVERT: K 19 GLU cc_start: 0.8241 (mp0) cc_final: 0.7617 (mt-10) REVERT: K 26 CYS cc_start: 0.8896 (p) cc_final: 0.8452 (m) REVERT: K 54 TYR cc_start: 0.8350 (m-80) cc_final: 0.8001 (m-10) REVERT: K 74 TYR cc_start: 0.8410 (t80) cc_final: 0.8049 (t80) REVERT: K 83 GLN cc_start: 0.8593 (tp40) cc_final: 0.8148 (tp-100) REVERT: K 124 GLU cc_start: 0.8119 (tp30) cc_final: 0.7771 (tm-30) REVERT: K 147 MET cc_start: 0.8654 (ppp) cc_final: 0.8063 (ppp) REVERT: K 183 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8576 (ttpp) REVERT: K 193 GLN cc_start: 0.8295 (tp40) cc_final: 0.7479 (tm-30) REVERT: K 197 ASP cc_start: 0.8297 (t0) cc_final: 0.8084 (m-30) REVERT: K 266 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8783 (mmmm) REVERT: K 285 LEU cc_start: 0.8904 (mm) cc_final: 0.8675 (mt) REVERT: K 317 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7580 (tp30) REVERT: K 327 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7859 (tpp) REVERT: S 27 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8247 (mt-10) REVERT: S 69 ASP cc_start: 0.7914 (t0) cc_final: 0.7452 (t0) REVERT: S 98 ASP cc_start: 0.8042 (p0) cc_final: 0.7781 (p0) REVERT: S 121 ARG cc_start: 0.6576 (ttt-90) cc_final: 0.6083 (tpt-90) REVERT: S 129 CYS cc_start: 0.8773 (p) cc_final: 0.8562 (p) REVERT: S 220 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8267 (tp30) REVERT: S 228 ASN cc_start: 0.9107 (m-40) cc_final: 0.8827 (m-40) REVERT: S 251 ASP cc_start: 0.6711 (t0) cc_final: 0.6489 (t0) REVERT: S 259 LEU cc_start: 0.8806 (mp) cc_final: 0.8575 (mp) REVERT: S 326 LYS cc_start: 0.8824 (pptt) cc_final: 0.8543 (pttp) REVERT: S 411 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7791 (mm-30) REVERT: S 413 MET cc_start: 0.8342 (mmm) cc_final: 0.7798 (mmm) REVERT: S 414 GLU cc_start: 0.7210 (pt0) cc_final: 0.6789 (mt-10) REVERT: S 417 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7969 (mt-10) REVERT: N 20 MET cc_start: 0.8601 (mtm) cc_final: 0.8066 (mtm) REVERT: N 148 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: N 201 LYS cc_start: 0.9101 (tttt) cc_final: 0.8895 (tppp) REVERT: N 210 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.4675 (ppp) REVERT: N 217 SER cc_start: 0.8883 (p) cc_final: 0.8243 (p) REVERT: N 248 ASP cc_start: 0.8294 (t0) cc_final: 0.7498 (t0) REVERT: N 254 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7248 (mtt90) REVERT: N 285 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9005 (mp) REVERT: N 346 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8083 (mtp85) outliers start: 56 outliers final: 36 residues processed: 501 average time/residue: 0.3552 time to fit residues: 275.2091 Evaluate side-chains 496 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 454 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 142 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS E 128 GLN I 100 ASN K 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089302 restraints weight = 41709.620| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.64 r_work: 0.3188 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24262 Z= 0.165 Angle : 0.565 8.193 32932 Z= 0.283 Chirality : 0.044 0.280 3616 Planarity : 0.004 0.049 4281 Dihedral : 9.289 179.505 3605 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.85 % Allowed : 16.06 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 2974 helix: 2.05 (0.15), residues: 1248 sheet: 0.11 (0.22), residues: 530 loop : -0.92 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.017 0.001 PHE B 367 TYR 0.018 0.001 TYR K 189 ARG 0.006 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1118) hydrogen bonds : angle 4.04041 ( 3417) covalent geometry : bond 0.00374 (24262) covalent geometry : angle 0.56464 (32932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 475 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8222 (t0) cc_final: 0.7829 (t0) REVERT: A 154 MET cc_start: 0.8869 (mmm) cc_final: 0.8663 (mmm) REVERT: A 215 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7972 (ttp-110) REVERT: A 254 GLU cc_start: 0.4224 (mm-30) cc_final: 0.2562 (mm-30) REVERT: A 284 GLU cc_start: 0.7078 (mp0) cc_final: 0.6710 (mt-10) REVERT: B 203 ASP cc_start: 0.8061 (t0) cc_final: 0.7745 (t0) REVERT: B 288 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 291 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7904 (tp-100) REVERT: E 24 TYR cc_start: 0.8127 (m-80) cc_final: 0.7353 (m-80) REVERT: E 33 ASP cc_start: 0.8768 (t0) cc_final: 0.8549 (t0) REVERT: E 123 ARG cc_start: 0.8764 (ttp-110) cc_final: 0.8229 (ttm-80) REVERT: E 276 ILE cc_start: 0.9212 (tt) cc_final: 0.8961 (tt) REVERT: E 398 MET cc_start: 0.7777 (ttm) cc_final: 0.7475 (mtp) REVERT: I 31 ASP cc_start: 0.8219 (t70) cc_final: 0.7936 (t0) REVERT: I 131 GLN cc_start: 0.8399 (tt0) cc_final: 0.7695 (tt0) REVERT: I 155 ILE cc_start: 0.9004 (mt) cc_final: 0.8746 (mm) REVERT: I 164 MET cc_start: 0.8514 (tpp) cc_final: 0.8266 (tpt) REVERT: I 230 SER cc_start: 0.8929 (m) cc_final: 0.8617 (t) REVERT: I 374 ILE cc_start: 0.9329 (tp) cc_final: 0.9022 (tt) REVERT: I 424 GLN cc_start: 0.8882 (tt0) cc_final: 0.8579 (tt0) REVERT: K 19 GLU cc_start: 0.8147 (mp0) cc_final: 0.7233 (mt-10) REVERT: K 26 CYS cc_start: 0.8918 (p) cc_final: 0.8499 (m) REVERT: K 55 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8452 (t) REVERT: K 74 TYR cc_start: 0.8453 (t80) cc_final: 0.8070 (t80) REVERT: K 83 GLN cc_start: 0.8762 (tp40) cc_final: 0.8333 (tp-100) REVERT: K 87 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: K 116 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7308 (mm110) REVERT: K 124 GLU cc_start: 0.8301 (tp30) cc_final: 0.7869 (tm-30) REVERT: K 147 MET cc_start: 0.8665 (ppp) cc_final: 0.8044 (ppp) REVERT: K 193 GLN cc_start: 0.8272 (tp40) cc_final: 0.7724 (tp40) REVERT: K 266 LYS cc_start: 0.9072 (mtpt) cc_final: 0.8792 (mmmm) REVERT: K 287 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8628 (tp30) REVERT: K 288 MET cc_start: 0.8628 (tmm) cc_final: 0.8267 (ttp) REVERT: K 317 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7616 (tp30) REVERT: K 327 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7882 (tpp) REVERT: K 353 GLN cc_start: 0.8537 (mp10) cc_final: 0.7619 (mp10) REVERT: S 27 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8275 (mt-10) REVERT: S 69 ASP cc_start: 0.7946 (t0) cc_final: 0.7458 (t0) REVERT: S 98 ASP cc_start: 0.8029 (p0) cc_final: 0.7717 (p0) REVERT: S 121 ARG cc_start: 0.6590 (ttt-90) cc_final: 0.6063 (tpt-90) REVERT: S 161 TYR cc_start: 0.8833 (m-80) cc_final: 0.8568 (m-80) REVERT: S 228 ASN cc_start: 0.9119 (m-40) cc_final: 0.8842 (m-40) REVERT: S 259 LEU cc_start: 0.8855 (mp) cc_final: 0.8642 (mp) REVERT: S 279 GLU cc_start: 0.8380 (tp30) cc_final: 0.7801 (tp30) REVERT: S 326 LYS cc_start: 0.8868 (pptt) cc_final: 0.8585 (pttp) REVERT: S 411 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7788 (mm-30) REVERT: S 413 MET cc_start: 0.8400 (mmm) cc_final: 0.7657 (mmm) REVERT: S 414 GLU cc_start: 0.7286 (pt0) cc_final: 0.6953 (mt-10) REVERT: S 417 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7938 (tt0) REVERT: N 20 MET cc_start: 0.8615 (mtm) cc_final: 0.8088 (mtm) REVERT: N 148 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: N 152 GLU cc_start: 0.8796 (mp0) cc_final: 0.8297 (mp0) REVERT: N 180 ASP cc_start: 0.8037 (t0) cc_final: 0.7680 (t0) REVERT: N 201 LYS cc_start: 0.9123 (tttt) cc_final: 0.8912 (tppp) REVERT: N 210 MET cc_start: 0.5066 (OUTLIER) cc_final: 0.4813 (ppp) REVERT: N 217 SER cc_start: 0.8898 (p) cc_final: 0.8257 (p) REVERT: N 248 ASP cc_start: 0.8304 (t0) cc_final: 0.7428 (t0) REVERT: N 285 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9000 (mp) REVERT: N 346 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8073 (mtp85) outliers start: 65 outliers final: 45 residues processed: 506 average time/residue: 0.3610 time to fit residues: 283.0849 Evaluate side-chains 506 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 454 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 378 LEU Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 34 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 242 optimal weight: 0.0970 chunk 282 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 347 ASN I 100 ASN K 70 GLN K 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.117195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089186 restraints weight = 58556.583| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.25 r_work: 0.3160 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24262 Z= 0.123 Angle : 0.544 8.472 32932 Z= 0.273 Chirality : 0.043 0.246 3616 Planarity : 0.004 0.048 4281 Dihedral : 9.107 179.573 3605 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 16.61 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2974 helix: 2.10 (0.15), residues: 1252 sheet: 0.16 (0.22), residues: 531 loop : -0.95 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.003 0.001 HIS K 84 PHE 0.017 0.001 PHE B 367 TYR 0.019 0.001 TYR K 189 ARG 0.007 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1118) hydrogen bonds : angle 3.95584 ( 3417) covalent geometry : bond 0.00275 (24262) covalent geometry : angle 0.54446 (32932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 491 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8318 (t0) cc_final: 0.8016 (t0) REVERT: A 93 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7782 (mt) REVERT: A 154 MET cc_start: 0.8905 (mmm) cc_final: 0.8692 (mmm) REVERT: A 196 GLU cc_start: 0.8829 (tp30) cc_final: 0.8462 (tt0) REVERT: A 254 GLU cc_start: 0.4235 (mm-30) cc_final: 0.2638 (mm-30) REVERT: A 284 GLU cc_start: 0.7146 (mp0) cc_final: 0.6833 (mt-10) REVERT: A 388 TRP cc_start: 0.8979 (m-10) cc_final: 0.8345 (m-10) REVERT: A 396 ASP cc_start: 0.8342 (m-30) cc_final: 0.8009 (m-30) REVERT: B 203 ASP cc_start: 0.8107 (t0) cc_final: 0.7814 (t0) REVERT: B 288 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: B 291 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7932 (tp-100) REVERT: E 24 TYR cc_start: 0.8310 (m-80) cc_final: 0.7327 (m-80) REVERT: E 123 ARG cc_start: 0.8791 (ttp-110) cc_final: 0.8245 (ttm-80) REVERT: E 276 ILE cc_start: 0.9237 (tt) cc_final: 0.8984 (tt) REVERT: E 339 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8646 (ttm-80) REVERT: I 26 ASP cc_start: 0.8517 (t70) cc_final: 0.8306 (t70) REVERT: I 31 ASP cc_start: 0.8284 (t70) cc_final: 0.7923 (t0) REVERT: I 131 GLN cc_start: 0.8432 (tt0) cc_final: 0.7787 (tp40) REVERT: I 155 ILE cc_start: 0.9027 (mt) cc_final: 0.8731 (mm) REVERT: I 230 SER cc_start: 0.8925 (m) cc_final: 0.8634 (t) REVERT: I 374 ILE cc_start: 0.9296 (tp) cc_final: 0.9050 (tt) REVERT: I 424 GLN cc_start: 0.8910 (tt0) cc_final: 0.8601 (tt0) REVERT: K 19 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: K 26 CYS cc_start: 0.8966 (p) cc_final: 0.8522 (m) REVERT: K 30 MET cc_start: 0.7550 (ttm) cc_final: 0.6964 (ttm) REVERT: K 54 TYR cc_start: 0.8282 (m-80) cc_final: 0.8009 (m-10) REVERT: K 74 TYR cc_start: 0.8462 (t80) cc_final: 0.8182 (t80) REVERT: K 83 GLN cc_start: 0.8799 (tp40) cc_final: 0.8388 (tp-100) REVERT: K 87 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: K 124 GLU cc_start: 0.8301 (tp30) cc_final: 0.7884 (tm-30) REVERT: K 147 MET cc_start: 0.8720 (ppp) cc_final: 0.8139 (ppp) REVERT: K 193 GLN cc_start: 0.7915 (tp40) cc_final: 0.7711 (tp40) REVERT: K 266 LYS cc_start: 0.9078 (mtpt) cc_final: 0.8806 (mmmm) REVERT: K 287 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8582 (tp30) REVERT: K 288 MET cc_start: 0.8748 (tmm) cc_final: 0.8496 (ttp) REVERT: K 317 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7749 (tp30) REVERT: K 327 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7911 (tpp) REVERT: S 27 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8263 (mt-10) REVERT: S 69 ASP cc_start: 0.7992 (t0) cc_final: 0.7443 (t0) REVERT: S 98 ASP cc_start: 0.8057 (p0) cc_final: 0.7808 (p0) REVERT: S 228 ASN cc_start: 0.9158 (m-40) cc_final: 0.8874 (m-40) REVERT: S 259 LEU cc_start: 0.8853 (mp) cc_final: 0.8629 (mp) REVERT: S 279 GLU cc_start: 0.8453 (tp30) cc_final: 0.7951 (tp30) REVERT: S 326 LYS cc_start: 0.8891 (pptt) cc_final: 0.8617 (pttp) REVERT: S 411 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7847 (mm-30) REVERT: S 413 MET cc_start: 0.8363 (mmm) cc_final: 0.7927 (mmm) REVERT: S 414 GLU cc_start: 0.7332 (pt0) cc_final: 0.7050 (mt-10) REVERT: S 417 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8072 (tt0) REVERT: N 20 MET cc_start: 0.8652 (mtm) cc_final: 0.8304 (mtm) REVERT: N 148 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: N 180 ASP cc_start: 0.8069 (t0) cc_final: 0.7774 (t0) REVERT: N 201 LYS cc_start: 0.9088 (tttt) cc_final: 0.8886 (tppp) REVERT: N 210 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4958 (ppp) REVERT: N 217 SER cc_start: 0.8906 (p) cc_final: 0.8288 (p) REVERT: N 248 ASP cc_start: 0.8335 (t0) cc_final: 0.7432 (t0) REVERT: N 285 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9044 (mp) REVERT: N 319 LEU cc_start: 0.9196 (mt) cc_final: 0.8938 (mm) REVERT: N 346 ARG cc_start: 0.8801 (mtp85) cc_final: 0.8090 (mtp85) outliers start: 60 outliers final: 43 residues processed: 516 average time/residue: 0.3585 time to fit residues: 287.3633 Evaluate side-chains 518 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 467 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 38 optimal weight: 0.7980 chunk 290 optimal weight: 0.7980 chunk 275 optimal weight: 0.0060 chunk 11 optimal weight: 0.5980 chunk 282 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 0.0040 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN I 100 ASN I 131 GLN K 230 HIS S 31 GLN N 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092542 restraints weight = 57892.564| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.23 r_work: 0.3200 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24262 Z= 0.103 Angle : 0.539 7.620 32932 Z= 0.271 Chirality : 0.042 0.227 3616 Planarity : 0.004 0.047 4281 Dihedral : 8.914 179.620 3605 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 2.62 % Allowed : 16.88 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2974 helix: 2.17 (0.15), residues: 1251 sheet: 0.25 (0.22), residues: 524 loop : -0.94 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.005 0.001 HIS N 59 PHE 0.025 0.001 PHE S 395 TYR 0.020 0.001 TYR K 189 ARG 0.006 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 1118) hydrogen bonds : angle 3.90703 ( 3417) covalent geometry : bond 0.00223 (24262) covalent geometry : angle 0.53905 (32932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 494 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8282 (t0) cc_final: 0.7928 (t0) REVERT: A 196 GLU cc_start: 0.8806 (tp30) cc_final: 0.8443 (tt0) REVERT: A 254 GLU cc_start: 0.4125 (mm-30) cc_final: 0.2232 (mm-30) REVERT: A 284 GLU cc_start: 0.7131 (mp0) cc_final: 0.6806 (mt-10) REVERT: A 388 TRP cc_start: 0.8942 (m-10) cc_final: 0.8323 (m-10) REVERT: B 170 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: B 203 ASP cc_start: 0.8058 (t0) cc_final: 0.7762 (t0) REVERT: B 288 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: B 291 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7892 (tp-100) REVERT: B 323 MET cc_start: 0.8381 (mmm) cc_final: 0.8077 (mmt) REVERT: E 24 TYR cc_start: 0.8288 (m-80) cc_final: 0.7349 (m-80) REVERT: E 123 ARG cc_start: 0.8765 (ttp-110) cc_final: 0.8177 (ttm-80) REVERT: E 276 ILE cc_start: 0.9239 (tt) cc_final: 0.9003 (tt) REVERT: E 322 ASP cc_start: 0.8801 (t0) cc_final: 0.8406 (t0) REVERT: I 31 ASP cc_start: 0.8256 (t70) cc_final: 0.7928 (t0) REVERT: I 131 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7756 (tp40) REVERT: I 155 ILE cc_start: 0.8999 (mt) cc_final: 0.8758 (mm) REVERT: I 230 SER cc_start: 0.8854 (m) cc_final: 0.8559 (t) REVERT: I 343 GLU cc_start: 0.8950 (pt0) cc_final: 0.8531 (pp20) REVERT: I 424 GLN cc_start: 0.8866 (tt0) cc_final: 0.8571 (tt0) REVERT: K 19 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: K 26 CYS cc_start: 0.8932 (p) cc_final: 0.8537 (m) REVERT: K 72 GLN cc_start: 0.8563 (tt0) cc_final: 0.8268 (pt0) REVERT: K 74 TYR cc_start: 0.8461 (t80) cc_final: 0.8175 (t80) REVERT: K 83 GLN cc_start: 0.8770 (tp40) cc_final: 0.8336 (tp-100) REVERT: K 87 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: K 112 GLU cc_start: 0.8366 (mp0) cc_final: 0.7964 (mp0) REVERT: K 124 GLU cc_start: 0.8289 (tp30) cc_final: 0.7934 (tm-30) REVERT: K 147 MET cc_start: 0.8695 (ppp) cc_final: 0.8181 (ppp) REVERT: K 266 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8775 (mmmm) REVERT: K 287 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8562 (tp30) REVERT: K 288 MET cc_start: 0.8782 (tmm) cc_final: 0.8554 (ttp) REVERT: K 317 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7881 (tp30) REVERT: K 327 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8022 (tpp) REVERT: S 27 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8212 (mt-10) REVERT: S 69 ASP cc_start: 0.7921 (t0) cc_final: 0.7375 (t0) REVERT: S 121 ARG cc_start: 0.6295 (ttt-90) cc_final: 0.6043 (tpt-90) REVERT: S 154 MET cc_start: 0.9094 (mmm) cc_final: 0.8856 (mmm) REVERT: S 259 LEU cc_start: 0.8830 (mp) cc_final: 0.8608 (mp) REVERT: S 279 GLU cc_start: 0.8461 (tp30) cc_final: 0.7967 (tp30) REVERT: S 326 LYS cc_start: 0.8852 (pptt) cc_final: 0.8573 (pttp) REVERT: S 378 LEU cc_start: 0.8749 (mp) cc_final: 0.8451 (mm) REVERT: S 392 ASP cc_start: 0.8735 (m-30) cc_final: 0.8443 (m-30) REVERT: S 411 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7886 (mm-30) REVERT: S 413 MET cc_start: 0.8266 (mmm) cc_final: 0.7884 (mmm) REVERT: S 414 GLU cc_start: 0.7198 (pt0) cc_final: 0.6957 (mt-10) REVERT: S 417 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8031 (tt0) REVERT: N 20 MET cc_start: 0.8689 (mtm) cc_final: 0.8356 (mtm) REVERT: N 72 GLN cc_start: 0.7157 (tp40) cc_final: 0.6897 (tp40) REVERT: N 148 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: N 152 GLU cc_start: 0.8813 (mp0) cc_final: 0.8391 (mp0) REVERT: N 180 ASP cc_start: 0.8092 (t0) cc_final: 0.7797 (t0) REVERT: N 201 LYS cc_start: 0.9086 (tttt) cc_final: 0.8876 (tppp) REVERT: N 210 MET cc_start: 0.5216 (OUTLIER) cc_final: 0.4953 (ppp) REVERT: N 217 SER cc_start: 0.8881 (p) cc_final: 0.8230 (p) REVERT: N 248 ASP cc_start: 0.8224 (t0) cc_final: 0.7420 (t0) REVERT: N 285 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8985 (mp) REVERT: N 319 LEU cc_start: 0.9163 (mt) cc_final: 0.8937 (mm) REVERT: N 346 ARG cc_start: 0.8723 (mtp85) cc_final: 0.7949 (mtp85) outliers start: 59 outliers final: 36 residues processed: 520 average time/residue: 0.3533 time to fit residues: 284.4500 Evaluate side-chains 530 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 485 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 100 ASN K 98 GLN S 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.115706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087941 restraints weight = 60513.865| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.23 r_work: 0.3145 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24262 Z= 0.191 Angle : 0.598 11.238 32932 Z= 0.300 Chirality : 0.044 0.248 3616 Planarity : 0.004 0.049 4281 Dihedral : 9.010 177.916 3601 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 2.85 % Allowed : 17.43 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 2974 helix: 2.17 (0.15), residues: 1241 sheet: 0.21 (0.22), residues: 537 loop : -1.00 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 344 HIS 0.005 0.001 HIS A 88 PHE 0.024 0.002 PHE K 52 TYR 0.027 0.001 TYR K 189 ARG 0.014 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1118) hydrogen bonds : angle 4.02924 ( 3417) covalent geometry : bond 0.00435 (24262) covalent geometry : angle 0.59811 (32932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 476 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8347 (t0) cc_final: 0.8063 (t0) REVERT: A 163 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8585 (mmmm) REVERT: A 196 GLU cc_start: 0.8848 (tp30) cc_final: 0.8486 (tt0) REVERT: A 205 ASP cc_start: 0.7383 (t0) cc_final: 0.7147 (t0) REVERT: A 254 GLU cc_start: 0.4262 (mm-30) cc_final: 0.2361 (mm-30) REVERT: A 284 GLU cc_start: 0.7151 (mp0) cc_final: 0.6832 (mt-10) REVERT: A 388 TRP cc_start: 0.9036 (m-10) cc_final: 0.8368 (m-10) REVERT: A 396 ASP cc_start: 0.8378 (m-30) cc_final: 0.8078 (m-30) REVERT: B 203 ASP cc_start: 0.8109 (t0) cc_final: 0.7907 (t0) REVERT: B 288 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 291 GLN cc_start: 0.8357 (tp-100) cc_final: 0.7695 (tp-100) REVERT: B 293 MET cc_start: 0.9075 (ttm) cc_final: 0.8834 (mtp) REVERT: E 24 TYR cc_start: 0.8306 (m-80) cc_final: 0.7388 (m-80) REVERT: E 123 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8299 (ttm-80) REVERT: E 276 ILE cc_start: 0.9268 (tt) cc_final: 0.8994 (tt) REVERT: E 398 MET cc_start: 0.8518 (tpp) cc_final: 0.7822 (mmm) REVERT: I 31 ASP cc_start: 0.8336 (t70) cc_final: 0.8048 (t0) REVERT: I 131 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: I 147 MET cc_start: 0.8785 (mtp) cc_final: 0.8563 (mtp) REVERT: I 155 ILE cc_start: 0.9013 (mt) cc_final: 0.8759 (mm) REVERT: I 230 SER cc_start: 0.8927 (m) cc_final: 0.8658 (t) REVERT: I 424 GLN cc_start: 0.8921 (tt0) cc_final: 0.8612 (tt0) REVERT: K 26 CYS cc_start: 0.8998 (p) cc_final: 0.8519 (m) REVERT: K 72 GLN cc_start: 0.8588 (tt0) cc_final: 0.8253 (pt0) REVERT: K 83 GLN cc_start: 0.8765 (tp40) cc_final: 0.8417 (tp-100) REVERT: K 124 GLU cc_start: 0.8343 (tp30) cc_final: 0.8054 (tm-30) REVERT: K 147 MET cc_start: 0.8706 (ppp) cc_final: 0.8155 (ppp) REVERT: K 266 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8773 (mmmm) REVERT: K 287 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8558 (tp30) REVERT: K 288 MET cc_start: 0.8802 (tmm) cc_final: 0.8583 (ttp) REVERT: K 289 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7444 (t0) REVERT: K 317 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7731 (tp30) REVERT: K 327 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7927 (tpp) REVERT: S 27 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8292 (mt-10) REVERT: S 121 ARG cc_start: 0.6506 (ttt-90) cc_final: 0.6103 (tpt-90) REVERT: S 259 LEU cc_start: 0.8841 (mp) cc_final: 0.8616 (mp) REVERT: S 279 GLU cc_start: 0.8594 (tp30) cc_final: 0.8108 (tp30) REVERT: S 326 LYS cc_start: 0.8979 (pptt) cc_final: 0.8707 (pttp) REVERT: S 411 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7863 (mm-30) REVERT: S 413 MET cc_start: 0.8373 (mmm) cc_final: 0.7972 (mmm) REVERT: S 414 GLU cc_start: 0.7249 (pt0) cc_final: 0.7007 (mt-10) REVERT: S 417 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (tt0) REVERT: N 20 MET cc_start: 0.8741 (mtm) cc_final: 0.8424 (mtm) REVERT: N 72 GLN cc_start: 0.7265 (tp40) cc_final: 0.6963 (tp40) REVERT: N 148 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: N 152 GLU cc_start: 0.8873 (mp0) cc_final: 0.8502 (mp0) REVERT: N 180 ASP cc_start: 0.8128 (t0) cc_final: 0.7874 (t0) REVERT: N 210 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.5118 (ppp) REVERT: N 217 SER cc_start: 0.8894 (p) cc_final: 0.8268 (p) REVERT: N 248 ASP cc_start: 0.8311 (t0) cc_final: 0.7464 (t0) REVERT: N 285 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8957 (mp) REVERT: N 319 LEU cc_start: 0.9209 (mt) cc_final: 0.8976 (mm) REVERT: N 346 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8035 (mtp85) outliers start: 65 outliers final: 43 residues processed: 505 average time/residue: 0.3726 time to fit residues: 292.3262 Evaluate side-chains 520 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 470 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 377 MET Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 93 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090579 restraints weight = 43651.420| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.65 r_work: 0.3193 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 24262 Z= 0.176 Angle : 0.730 59.200 32932 Z= 0.397 Chirality : 0.043 0.242 3616 Planarity : 0.004 0.049 4281 Dihedral : 9.011 177.784 3601 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.42 % Allowed : 18.01 % Favored : 79.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2974 helix: 2.19 (0.15), residues: 1241 sheet: 0.20 (0.22), residues: 537 loop : -0.99 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 344 HIS 0.004 0.001 HIS E 192 PHE 0.021 0.001 PHE K 52 TYR 0.023 0.001 TYR K 189 ARG 0.011 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1118) hydrogen bonds : angle 4.03098 ( 3417) covalent geometry : bond 0.00383 (24262) covalent geometry : angle 0.72982 (32932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 469 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8285 (t0) cc_final: 0.7992 (t0) REVERT: A 154 MET cc_start: 0.8816 (mmm) cc_final: 0.8477 (mmm) REVERT: A 163 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8565 (mmmm) REVERT: A 196 GLU cc_start: 0.8758 (tp30) cc_final: 0.8406 (tt0) REVERT: A 205 ASP cc_start: 0.7318 (t0) cc_final: 0.7080 (t0) REVERT: A 254 GLU cc_start: 0.4198 (mm-30) cc_final: 0.2292 (mm-30) REVERT: A 284 GLU cc_start: 0.7058 (mp0) cc_final: 0.6759 (mt-10) REVERT: A 388 TRP cc_start: 0.9016 (m-10) cc_final: 0.8367 (m-10) REVERT: A 396 ASP cc_start: 0.8312 (m-30) cc_final: 0.8012 (m-30) REVERT: B 288 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: B 291 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7621 (tp-100) REVERT: B 293 MET cc_start: 0.9060 (ttm) cc_final: 0.8819 (mtp) REVERT: E 24 TYR cc_start: 0.8265 (m-80) cc_final: 0.7346 (m-80) REVERT: E 123 ARG cc_start: 0.8789 (ttp-110) cc_final: 0.8268 (ttm-80) REVERT: E 276 ILE cc_start: 0.9251 (tt) cc_final: 0.8972 (tt) REVERT: E 398 MET cc_start: 0.8482 (tpp) cc_final: 0.7777 (mmm) REVERT: I 31 ASP cc_start: 0.8264 (t70) cc_final: 0.7983 (t0) REVERT: I 131 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7544 (tp40) REVERT: I 147 MET cc_start: 0.8714 (mtp) cc_final: 0.8484 (mtp) REVERT: I 155 ILE cc_start: 0.8997 (mt) cc_final: 0.8736 (mm) REVERT: I 230 SER cc_start: 0.8880 (m) cc_final: 0.8612 (t) REVERT: I 424 GLN cc_start: 0.8873 (tt0) cc_final: 0.8545 (tt0) REVERT: K 26 CYS cc_start: 0.8954 (p) cc_final: 0.8487 (m) REVERT: K 72 GLN cc_start: 0.8584 (tt0) cc_final: 0.8234 (pt0) REVERT: K 83 GLN cc_start: 0.8749 (tp40) cc_final: 0.8398 (tp-100) REVERT: K 124 GLU cc_start: 0.8308 (tp30) cc_final: 0.8033 (tm-30) REVERT: K 147 MET cc_start: 0.8677 (ppp) cc_final: 0.8124 (ppp) REVERT: K 266 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8748 (mmmm) REVERT: K 287 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8523 (tp30) REVERT: K 288 MET cc_start: 0.8768 (tmm) cc_final: 0.8545 (ttp) REVERT: K 289 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7376 (t0) REVERT: K 317 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7683 (tp30) REVERT: K 327 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7879 (tpp) REVERT: S 27 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8235 (mt-10) REVERT: S 121 ARG cc_start: 0.6456 (ttt-90) cc_final: 0.6040 (tpt-90) REVERT: S 128 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8088 (tm-30) REVERT: S 154 MET cc_start: 0.9051 (mmm) cc_final: 0.8782 (mmm) REVERT: S 259 LEU cc_start: 0.8805 (mp) cc_final: 0.8575 (mp) REVERT: S 279 GLU cc_start: 0.8531 (tp30) cc_final: 0.8039 (tp30) REVERT: S 326 LYS cc_start: 0.8939 (pptt) cc_final: 0.8658 (pttp) REVERT: S 390 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7779 (mtp180) REVERT: S 411 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7815 (mm-30) REVERT: S 413 MET cc_start: 0.8331 (mmm) cc_final: 0.7919 (mmm) REVERT: S 414 GLU cc_start: 0.7203 (pt0) cc_final: 0.6974 (mt-10) REVERT: S 417 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8066 (tt0) REVERT: N 20 MET cc_start: 0.8708 (mtm) cc_final: 0.8400 (mtm) REVERT: N 148 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: N 152 GLU cc_start: 0.8822 (mp0) cc_final: 0.8442 (mp0) REVERT: N 180 ASP cc_start: 0.8059 (t0) cc_final: 0.7804 (t0) REVERT: N 210 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.5086 (ppp) REVERT: N 217 SER cc_start: 0.8875 (p) cc_final: 0.8214 (p) REVERT: N 248 ASP cc_start: 0.8269 (t0) cc_final: 0.7406 (t0) REVERT: N 285 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8937 (mp) REVERT: N 319 LEU cc_start: 0.9197 (mt) cc_final: 0.8961 (mm) REVERT: N 346 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8019 (mtp85) outliers start: 54 outliers final: 45 residues processed: 492 average time/residue: 0.3616 time to fit residues: 275.0057 Evaluate side-chains 517 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 465 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 108 optimal weight: 0.3980 chunk 189 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 281 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS I 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090671 restraints weight = 42434.016| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.61 r_work: 0.3196 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 24262 Z= 0.176 Angle : 0.730 59.200 32932 Z= 0.397 Chirality : 0.043 0.242 3616 Planarity : 0.004 0.049 4281 Dihedral : 9.011 177.784 3601 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.34 % Allowed : 18.09 % Favored : 79.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2974 helix: 2.19 (0.15), residues: 1241 sheet: 0.20 (0.22), residues: 537 loop : -0.99 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 344 HIS 0.004 0.001 HIS E 192 PHE 0.021 0.001 PHE K 52 TYR 0.023 0.001 TYR K 189 ARG 0.011 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1118) hydrogen bonds : angle 4.03098 ( 3417) covalent geometry : bond 0.00383 (24262) covalent geometry : angle 0.72984 (32932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 466 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8489 (t0) cc_final: 0.8189 (t0) REVERT: A 154 MET cc_start: 0.8965 (mmm) cc_final: 0.8625 (mmm) REVERT: A 163 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8633 (mmmm) REVERT: A 196 GLU cc_start: 0.9003 (tp30) cc_final: 0.8643 (tt0) REVERT: A 205 ASP cc_start: 0.7560 (t0) cc_final: 0.7314 (t0) REVERT: A 254 GLU cc_start: 0.4405 (mm-30) cc_final: 0.2328 (mm-30) REVERT: A 284 GLU cc_start: 0.7342 (mp0) cc_final: 0.6975 (mt-10) REVERT: A 388 TRP cc_start: 0.9055 (m-10) cc_final: 0.8406 (m-10) REVERT: A 396 ASP cc_start: 0.8561 (m-30) cc_final: 0.8291 (m-30) REVERT: B 288 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: B 291 GLN cc_start: 0.8509 (tp-100) cc_final: 0.7867 (tp-100) REVERT: B 293 MET cc_start: 0.9085 (ttm) cc_final: 0.8851 (mtp) REVERT: E 24 TYR cc_start: 0.8411 (m-80) cc_final: 0.7500 (m-80) REVERT: E 123 ARG cc_start: 0.8938 (ttp-110) cc_final: 0.8380 (ttm-80) REVERT: E 276 ILE cc_start: 0.9314 (tt) cc_final: 0.9036 (tt) REVERT: E 398 MET cc_start: 0.8605 (tpp) cc_final: 0.7926 (mmm) REVERT: I 31 ASP cc_start: 0.8506 (t70) cc_final: 0.8202 (t0) REVERT: I 131 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7750 (tp40) REVERT: I 147 MET cc_start: 0.8937 (mtp) cc_final: 0.8729 (mtp) REVERT: I 155 ILE cc_start: 0.9096 (mt) cc_final: 0.8850 (mm) REVERT: I 230 SER cc_start: 0.8994 (m) cc_final: 0.8734 (t) REVERT: I 424 GLN cc_start: 0.9050 (tt0) cc_final: 0.8760 (tt0) REVERT: K 26 CYS cc_start: 0.9043 (p) cc_final: 0.8551 (m) REVERT: K 72 GLN cc_start: 0.8621 (tt0) cc_final: 0.8270 (pt0) REVERT: K 83 GLN cc_start: 0.8779 (tp40) cc_final: 0.8425 (tp-100) REVERT: K 124 GLU cc_start: 0.8392 (tp30) cc_final: 0.8087 (tm-30) REVERT: K 147 MET cc_start: 0.8757 (ppp) cc_final: 0.8230 (ppp) REVERT: K 266 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8829 (mmmm) REVERT: K 287 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8650 (tp30) REVERT: K 288 MET cc_start: 0.8860 (tmm) cc_final: 0.8624 (ttp) REVERT: K 289 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7599 (t0) REVERT: K 317 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7843 (tp30) REVERT: K 327 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8042 (tpp) REVERT: S 27 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8395 (mt-10) REVERT: S 121 ARG cc_start: 0.6618 (ttt-90) cc_final: 0.6006 (tpt-90) REVERT: S 128 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8176 (tm-30) REVERT: S 154 MET cc_start: 0.9140 (mmm) cc_final: 0.8878 (mmm) REVERT: S 259 LEU cc_start: 0.8903 (mp) cc_final: 0.8688 (mp) REVERT: S 279 GLU cc_start: 0.8683 (tp30) cc_final: 0.8187 (tp30) REVERT: S 326 LYS cc_start: 0.9045 (pptt) cc_final: 0.8783 (pttp) REVERT: S 390 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.7946 (mtp180) REVERT: S 392 ASP cc_start: 0.8800 (m-30) cc_final: 0.8532 (m-30) REVERT: S 411 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7985 (mm-30) REVERT: S 413 MET cc_start: 0.8465 (mmm) cc_final: 0.8048 (mmm) REVERT: S 414 GLU cc_start: 0.7329 (pt0) cc_final: 0.7062 (mt-10) REVERT: S 417 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8161 (tt0) REVERT: N 20 MET cc_start: 0.8768 (mtm) cc_final: 0.8452 (mtm) REVERT: N 148 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: N 152 GLU cc_start: 0.8988 (mp0) cc_final: 0.8622 (mp0) REVERT: N 180 ASP cc_start: 0.8239 (t0) cc_final: 0.7974 (t0) REVERT: N 210 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.5202 (ppp) REVERT: N 217 SER cc_start: 0.8964 (p) cc_final: 0.8405 (p) REVERT: N 248 ASP cc_start: 0.8427 (t0) cc_final: 0.7616 (t0) REVERT: N 285 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9021 (mp) REVERT: N 319 LEU cc_start: 0.9226 (mt) cc_final: 0.9001 (mm) REVERT: N 346 ARG cc_start: 0.8879 (mtp85) cc_final: 0.8135 (mtp85) outliers start: 52 outliers final: 45 residues processed: 488 average time/residue: 0.3581 time to fit residues: 271.1568 Evaluate side-chains 517 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 465 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 191 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 246 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 230 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090111 restraints weight = 49950.007| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.86 r_work: 0.3174 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 24262 Z= 0.176 Angle : 0.730 59.200 32932 Z= 0.397 Chirality : 0.043 0.242 3616 Planarity : 0.004 0.049 4281 Dihedral : 9.011 177.784 3601 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.34 % Allowed : 18.13 % Favored : 79.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2974 helix: 2.19 (0.15), residues: 1241 sheet: 0.20 (0.22), residues: 537 loop : -0.99 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 344 HIS 0.004 0.001 HIS E 192 PHE 0.021 0.001 PHE K 52 TYR 0.023 0.001 TYR K 189 ARG 0.011 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1118) hydrogen bonds : angle 4.03098 ( 3417) covalent geometry : bond 0.00383 (24262) covalent geometry : angle 0.72984 (32932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14136.03 seconds wall clock time: 244 minutes 0.07 seconds (14640.07 seconds total)